Team:DTU Denmark/USERprograminstructions

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<p> 
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   The redoxilator<br><br>
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   The redoxilator<br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/theory" CLASS=leftbar>- Introduction</a><br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/genetic_design" CLASS=leftbar>- Genetic design</a><br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/yeast" CLASS=leftbar>- Results</a><br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/applications" CLASS=leftbar>- Applications and perspectives</a><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/practicalapproach" CLASS=leftbar>- Applications and perspectives</a><br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/safety" CLASS=leftbar>- Safety considerations</a><br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/safety" CLASS=leftbar>- Safety considerations</a><br><br>
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<p> 
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     <br>The USER<sup>TM</sup> assembly standard<br><br>
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     <br>The USER assembly standard<br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprinciple" CLASS=leftbar>- USER<sup>TM</sup> cloning</a><br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprinciple" CLASS=leftbar>- USER fusion of biobricks</a><br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/USERconcept" CLASS=leftbar>- USER<sup>TM</sup> fusion</a><br><br>
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<p> 
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     <br>USER<sup>TM</sup> fusion primer design software<br><br>
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     <br>USER fusion primer design software<br>
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     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>- Abstract</a><br>
     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogram" CLASS=leftbar>- Abstract</a><br>
     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprograminstructions" CLASS=leftbar>- Instructions</a><br>
     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprograminstructions" CLASS=leftbar>- Instructions</a><br>
     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogramoutputformat" CLASS=leftbar>- Output format</a><br>
     <a href="https://2009.igem.org/Team:DTU_Denmark/USERprogramoutputformat" CLASS=leftbar>- Output format</a><br>
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    <br>Experimental results<br>
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    <a href="https://2009.igem.org/Team:DTU_Denmark/results" CLASS=leftbar>- Results and discussion</a><br>
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   <b>The project</b><br><br><br>
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   <b>The project</b><br><br>
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<font size="4"><b>The USER fusion primer design software: PHUSER (<u>P</u>rimer <u>H</u>elp for <u>USER</u>)</b></font><br><br>
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<font size="4"><b>The USER fusion primer design software: PHUSER<br>(<u>P</u>rimer <u>H</u>elp for <u>USER</u>)</b></font><br><br>
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<font size="3"><b>Program user manual</b></font><br>
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<font size="3"><b>PHUSER user manual</b></font><br>
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<p align="justify">We have put a lot of thought and consideration into which user-definable parameters to include. In the end, we decided that a user-friendly input was the best solution for the beta version of the software. Further down the line, the program can be customized for high-end users, and advanced options made available upon request. For now we keep it simple, and ask only for three main inputs:</p><br>
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<p align="justify">We have put a lot of thought and consideration into which user-definable parameters to include. In the end, we decided that a user-friendly input was the best solution for the beta version of PHUSER. Further down the line, the program can be customized for high-end users, and advanced options made available upon request. For now we keep it simple, and ask only for three main inputs:</p><br>
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<b>1.</b>Name of biobrick (essentially you can call it whatever you wish), and;<br>
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<b>1. </b>Name of biobrick (essentially you can call it whatever you wish), and;<br>
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<b>2.</b>Sequence of biobrick (pasted as single-stranded DNA from 5' to 3'). <i>NOTE: Only A's, T's, G's, and C's are accepted as input, i.e. no FASTA-headers or spaces (line shifts are ok).</i><br>
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<b>2. </b>Sequence of biobrick (pasted as single-stranded DNA from 5' to 3'). <i>NOTE: Only A's, T's, G's, and C's are accepted as input, i.e. no FASTA-headers or spaces (line shifts are ok).</i><br>
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<b>3.</b>Your choice of USER cassette. For now only one is available, but more will follow shortly.<br><br>
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<b>3. </b>Your choice of USER cassette. For now only one is available, but more will follow shortly.<br><br>
<p align="justify">As a default in the interface, only two biobrick-submission boxes are available to begin with. If you wish to fuse more than two biobricks in the same reaction, simply click "add another biobrick" and another submission box will appear. The maximum capacity is nine biobricks (may be subject to change).</p><br>
<p align="justify">As a default in the interface, only two biobrick-submission boxes are available to begin with. If you wish to fuse more than two biobricks in the same reaction, simply click "add another biobrick" and another submission box will appear. The maximum capacity is nine biobricks (may be subject to change).</p><br>
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<a href="http://igem.grafiki.org/" CLASS=leftbar target="blank">Design your primers here</a><br><br>
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<b>Design your primers with PHUSER <a href="http://igem.grafiki.org/" CLASS=leftbar target="blank">here</a></b><br><br>
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  <b>Synthetic Biology</b><br><br>
 
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<p align="left"><i>“Synthetic Biology is an art of engineering new biological systems that don’t exist in nature.”</i><br></p>
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<strong>Achievements</strong><br>
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<br>
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<p align="right"><i>-Paras Chopra & Akhil Kamma</i><br><br></p>
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<strong>Redox sensing device</strong><br>
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Two novel genes have been designed and synthesized each comprised of 5 genetic elements. Together they function as a device termed the Redoxilator that can sense the internal redox state of a yeast cell, and output a reporter signal. Extensive mathematical modelling was performed to simulate how the construct would operate <i>in vivo</i>.<br>
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<br>
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<strong>Biobricks</strong><br>
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DNA of several new biobricks have been designed and submitted including a yeast optimized GFP reporter protein, a protein degradation sequence and a fast degradable yeast GFP. (Bronze medal)<br>
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<br>
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We have demonstrated that our USER fusion biobrick works as expected and documented it (silver medal)<br>
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<br>
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<strong>USER fusion Assembly standard</strong><br>
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A new biobrick assembly standard that allows the rapid construction of multi-part devices have been developed and documented. The assembly standard offers many benefits: All restriction sites are allowed, multiple biobricks can be joined in one step, the result is scar-free making it ideal for protein fusions and more. (Gold medal)<br>
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<br>
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<strong>USER-fusion primer design software</strong><br>
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A novel and very useful software tool have been developed that can automatically design the optimal primers for USER fusion assembly of 2-9 biobricks, taking several parameters into account.
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</p>
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<p>In nature, biological molecules work together in complex systems to serve purposes of the cell. In synthetic biology these molecules are used as individual functional units that are combined to form tailored systems exhibiting complex dynamical behaviour. From ‘design specifications’ generated from computational modelling, engineering-based approaches enables the construction of such new specified gene-regulatory networks. The ultimate goal of synthetic biology is to construct systems that gain new functions, and the perspectives of the technology are enormous. It has already been used in several medical projects2 and is predicted to play a major role in biotech-production and environmental aspects.</p>
 
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Latest revision as of 03:16, 22 October 2009

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The project

Home The Team The Project Parts submitted Modelling Notebook


The redoxilator

- Genetic design
- Applications and perspectives
- Safety considerations


The USER assembly standard

- USER fusion of biobricks


USER fusion primer design software

- Abstract
- Instructions
- Output format


Experimental results

- Results and discussion
The project

 The USER fusion primer design software: PHUSER
(Primer Help for USER)

PHUSER user manual

We have put a lot of thought and consideration into which user-definable parameters to include. In the end, we decided that a user-friendly input was the best solution for the beta version of PHUSER. Further down the line, the program can be customized for high-end users, and advanced options made available upon request. For now we keep it simple, and ask only for three main inputs:


1. Name of biobrick (essentially you can call it whatever you wish), and;
2. Sequence of biobrick (pasted as single-stranded DNA from 5' to 3'). NOTE: Only A's, T's, G's, and C's are accepted as input, i.e. no FASTA-headers or spaces (line shifts are ok).
3. Your choice of USER cassette. For now only one is available, but more will follow shortly.

As a default in the interface, only two biobrick-submission boxes are available to begin with. If you wish to fuse more than two biobricks in the same reaction, simply click "add another biobrick" and another submission box will appear. The maximum capacity is nine biobricks (may be subject to change).


Design your primers with PHUSER here

 		Achievements

Redox sensing device
Two novel genes have been designed and synthesized each comprised of 5 genetic elements. Together they function as a device termed the Redoxilator that can sense the internal redox state of a yeast cell, and output a reporter signal. Extensive mathematical modelling was performed to simulate how the construct would operate in vivo.

Biobricks
DNA of several new biobricks have been designed and submitted including a yeast optimized GFP reporter protein, a protein degradation sequence and a fast degradable yeast GFP. (Bronze medal)

We have demonstrated that our USER fusion biobrick works as expected and documented it (silver medal)

USER fusion Assembly standard
A new biobrick assembly standard that allows the rapid construction of multi-part devices have been developed and documented. The assembly standard offers many benefits: All restriction sites are allowed, multiple biobricks can be joined in one step, the result is scar-free making it ideal for protein fusions and more. (Gold medal)

USER-fusion primer design software
A novel and very useful software tool have been developed that can automatically design the optimal primers for USER fusion assembly of 2-9 biobricks, taking several parameters into account.

Comments or questions to the team? Please -- Comments of questions to webmaster? Please

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